Pyramidalization of a carbonyl C atom in (2S)-N-(seleno-acet-yl)proline methyl ester.

The title compound, C8H13NO2Se, crystallizes as a non-merohedral twin with an approximate 9:1 component ratio with two symmetry-independent mol-ecules in the asymmetric unit. Our density-functional theory (DFT) computations indicate that the carb-oxy C atom is expected to be slightly pyramidal due to an n→ π* inter-action, wherein the lone pair (n) of the Se atom overlap with the anti-bonding orbital (π*) of the carbonyl group. Such pyramidalization is observed in one mol-ecule of the title compound but not the other.

Related literature

For background to hybrid density functional theory (DFT) and natural bond orbital (NBO) analysis, see: Glendening et al. (2001 ▶); Weinhold (1998 ▶); Weinhold & Landis (2005 ▶). For literature related to the synthesis, see: Bhattacharyya & Woollins (2001 ▶) and for NBO studies of the title compound, see: Choudhary & Raines (2011a ▶); DeRider et al. (2002 ▶); Choudhary et al. (2009 ▶, 2010a ▶,b ▶); Jakobsche et al. (2010 ▶); Bartlett et al. (2010 ▶); Choudhary & Raines (2011b ▶). For geometrical checks with ConQuest and Mercury, see: Bruno et al. (2002 ▶). For Gaussian 03 software, see: Frisch (2004 ▶). For puckering parameters, see: Cremer & Pople (1975 ▶).

Experimental

Crystal data

C8H13NO2Se

M = 234.15

Triclinic,

a = 7.050 (3) Å

b = 7.442 (3) Å

c = 10.334 (4) Å

α = 85.166 (6)°

β = 86.220 (6)°

γ = 64.682 (4)°

V = 488.1 (3) Å3

Z = 2

Mo Kα radiation

μ = 3.81 mm−1

T = 105 K

0.47 × 0.37 × 0.35 mm

Data collection

Bruker SMART APEX2 area detector diffractometer

Absorption correction: multi-scan (TWINABS; Bruker, 2007 ▶) T min = 0.268, T max = 0.349

3012 measured reflections

3012 independent reflections

2938 reflections with I > 2σ(I)

Refinement

R[F 2 > 2σ(F 2)] = 0.051

wR(F 2) = 0.135

S = 1.12

3012 reflections

224 parameters

3 restraints

H-atom parameters constrained

Δρmax = 1.46 e Å−3

Δρmin = −0.63 e Å−3

Absolute structure: Classical Flack method preferred over Parsons because s.u. lower.

Flack parameter: 0.01 (3)

Data collection: APEX2 (Bruker, 2012 ▶); cell refinement: SAINT-Plus (Bruker, 2007 ▶); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXTL; molecular graphics: OLEX2 (Dolomanov et al., 2009 ▶) and NBOView (Wendt & Weinhold, 2001 ▶); software used to prepare material for publication: OLEX2, GX and FCF_filter (Guzei, 2012 ▶).

Click here for additional data file.

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536813011112/kj2221sup1.cif

Click here for additional data file.

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536813011112/kj2221Isup2.hkl

Click here for additional data file.

Supplementary material file. DOI: 10.1107/S1600536813011112/kj2221Isup3.cml

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

C8H13NO2Se	Z = 2
Mr = 234.15	F(000) = 236
Triclinic, P1	Dx = 1.593 Mg m−3
a = 7.050 (3) Å	Mo Kα radiation, λ = 0.71073 Å
b = 7.442 (3) Å	Cell parameters from 746 reflections
c = 10.334 (4) Å	θ = 3.0–29.0°
α = 85.166 (6)°	µ = 3.81 mm−1
β = 86.220 (6)°	T = 105 K
γ = 64.682 (4)°	Block, colourless
V = 488.1 (3) Å3	0.47 × 0.37 × 0.35 mm

Bruker SMART APEX2 area detector diffractometer	3012 measured reflections
Radiation source: microfocus sealed X-ray tube, Incoatec Iµs	3012 independent reflections
Mirror optics monochromator	2938 reflections with I > 2σ(I)
Detector resolution: 7.9 pixels mm-1	θmax = 25.1°, θmin = 2.0°
0.5° ω and 0.5° φ scans	h = −8→8
Absorption correction: multi-scan (TWINABS; Bruker, 2007)	k = −8→8
Tmin = 0.268, Tmax = 0.349	l = −12→12

Refinement on F2	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H-atom parameters constrained
R[F2 > 2σ(F2)] = 0.051	w = 1/[σ2(Fo2) + (0.0947P)2 + 1.2373P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.135	(Δ/σ)max < 0.001
S = 1.12	Δρmax = 1.46 e Å−3
3012 reflections	Δρmin = −0.63 e Å−3
224 parameters	Absolute structure: Classical Flack method preferred over Parsons because s.u. lower.
3 restraints	Flack parameter: 0.01 (3)

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refined as a 4-component twin.

	x	y	z	Uiso*/Ueq
Se1	1.02636 (11)	0.03198 (10)	0.80590 (9)	0.0268 (3)
O1	0.6582 (13)	0.5319 (12)	0.9097 (8)	0.0258 (17)
O2	0.6687 (15)	0.5834 (13)	0.6919 (8)	0.0267 (19)
N1	0.6036 (14)	0.1857 (14)	0.8793 (9)	0.0209 (18)
C1	0.807 (2)	−0.108 (2)	1.0113 (14)	0.024 (3)
H1A	0.7617	−0.0430	1.0937	0.036*
H1B	0.9523	−0.2093	1.0174	0.036*
H1C	0.7156	−0.1708	0.9932	0.036*
C2	0.7948 (17)	0.0453 (16)	0.9034 (12)	0.023 (2)
C3	0.4089 (18)	0.2096 (19)	0.9573 (12)	0.024 (3)
H3A	0.4309	0.2039	1.0515	0.029*
H3B	0.3636	0.1052	0.9401	0.029*
C4	0.2498 (18)	0.4141 (18)	0.9102 (13)	0.027 (3)
H4A	0.1058	0.4219	0.9172	0.032*
H4B	0.2550	0.5190	0.9608	0.032*
C5	0.3161 (18)	0.436 (2)	0.7695 (13)	0.028 (3)
H5A	0.2615	0.5776	0.7380	0.034*
H5B	0.2662	0.3647	0.7132	0.034*
C6	0.5599 (17)	0.3388 (16)	0.7724 (10)	0.020 (2)
H6	0.6241	0.2781	0.6885	0.024*
C7	0.6369 (17)	0.4933 (16)	0.8033 (11)	0.022 (2)
C8	0.734 (3)	0.740 (2)	0.7072 (15)	0.031 (3)
H8A	0.6159	0.8558	0.7411	0.046*
H8B	0.7828	0.7783	0.6228	0.046*
H8C	0.8493	0.6918	0.7681	0.046*
Se1A	1.07753 (15)	0.71492 (14)	0.39148 (11)	0.0314 (4)
O1A	0.5592 (13)	1.1157 (14)	0.2797 (8)	0.0279 (18)
O2A	0.5329 (13)	1.1213 (14)	0.4976 (9)	0.0264 (19)
N1A	0.9670 (14)	1.1015 (14)	0.2881 (9)	0.0212 (19)
C1A	1.259 (2)	0.861 (2)	0.1724 (16)	0.026 (3)
H1AA	1.1935	0.9144	0.0886	0.038*
H1AB	1.3372	0.7162	0.1715	0.038*
H1AC	1.3562	0.9199	0.1874	0.038*
C2A	1.0943 (16)	0.9115 (16)	0.2781 (11)	0.020 (2)
C3A	0.9718 (18)	1.2692 (17)	0.2000 (12)	0.025 (2)
H3AA	0.9716	1.2428	0.1077	0.030*
H3AB	1.0970	1.2921	0.2141	0.030*
C4A	0.771 (2)	1.446 (2)	0.2387 (14)	0.031 (3)
H4AA	0.7858	1.5722	0.2220	0.037*
H4AB	0.6505	1.4540	0.1904	0.037*
C5A	0.7423 (19)	1.4030 (19)	0.3828 (13)	0.031 (3)
H5AA	0.5938	1.4753	0.4120	0.037*
H5AB	0.8312	1.4416	0.4341	0.037*
C6A	0.8117 (17)	1.1760 (18)	0.3963 (11)	0.022 (2)
H6A	0.8771	1.1185	0.4819	0.027*
C7A	0.6233 (17)	1.1279 (17)	0.3787 (11)	0.023 (2)
C8A	0.347 (2)	1.085 (3)	0.4944 (16)	0.040 (4)
H8AA	0.2399	1.1934	0.4433	0.060*
H8AB	0.2912	1.0772	0.5832	0.060*
H8AC	0.3832	0.9585	0.4546	0.060*

	U11	U22	U33	U12	U13	U23
Se1	0.0198 (6)	0.0286 (7)	0.0363 (8)	−0.0150 (6)	0.0045 (5)	−0.0029 (5)
O1	0.028 (4)	0.027 (4)	0.026 (5)	−0.016 (4)	0.000 (3)	−0.004 (3)
O2	0.030 (5)	0.030 (5)	0.029 (5)	−0.021 (4)	−0.007 (4)	0.000 (3)
N1	0.020 (5)	0.021 (5)	0.026 (5)	−0.014 (4)	0.002 (3)	−0.001 (3)
C1	0.019 (6)	0.023 (7)	0.027 (7)	−0.007 (6)	−0.004 (5)	−0.001 (5)
C2	0.016 (5)	0.019 (5)	0.037 (7)	−0.008 (5)	0.000 (4)	−0.006 (4)
C3	0.020 (6)	0.022 (6)	0.035 (6)	−0.012 (5)	0.001 (5)	−0.004 (5)
C4	0.015 (5)	0.021 (6)	0.047 (7)	−0.011 (5)	0.001 (5)	−0.004 (5)
C5	0.021 (6)	0.020 (6)	0.045 (7)	−0.009 (5)	−0.010 (5)	0.002 (5)
C6	0.021 (5)	0.022 (5)	0.024 (5)	−0.015 (5)	−0.006 (4)	−0.002 (4)
C7	0.018 (5)	0.023 (6)	0.029 (6)	−0.011 (5)	−0.003 (4)	0.001 (4)
C8	0.039 (8)	0.025 (7)	0.039 (8)	−0.025 (6)	0.000 (6)	0.001 (5)
Se1A	0.0285 (7)	0.0247 (7)	0.0453 (9)	−0.0164 (6)	−0.0005 (6)	0.0041 (6)
O1A	0.019 (4)	0.039 (5)	0.030 (5)	−0.016 (4)	−0.001 (3)	−0.005 (4)
O2A	0.019 (4)	0.035 (5)	0.033 (5)	−0.019 (4)	−0.005 (3)	0.002 (3)
N1A	0.018 (5)	0.029 (5)	0.023 (5)	−0.018 (4)	−0.002 (3)	0.002 (4)
C1A	0.018 (6)	0.027 (7)	0.039 (8)	−0.018 (6)	0.003 (5)	0.000 (6)
C2A	0.015 (5)	0.022 (6)	0.028 (6)	−0.011 (5)	−0.012 (4)	0.000 (4)
C3A	0.022 (6)	0.019 (5)	0.039 (7)	−0.015 (5)	0.002 (5)	0.007 (5)
C4A	0.026 (7)	0.016 (7)	0.051 (8)	−0.011 (6)	−0.002 (6)	0.003 (6)
C5A	0.022 (6)	0.030 (7)	0.043 (8)	−0.013 (6)	0.004 (5)	−0.009 (6)
C6A	0.017 (5)	0.029 (7)	0.024 (6)	−0.012 (5)	−0.006 (4)	0.000 (5)
C7A	0.020 (6)	0.027 (6)	0.026 (6)	−0.014 (5)	0.004 (4)	−0.006 (4)
C8A	0.027 (7)	0.068 (12)	0.043 (8)	−0.038 (8)	0.010 (6)	−0.013 (8)

Se1—C2	1.831 (11)	Se1A—C2A	1.835 (11)
O1—C7	1.194 (14)	O1A—C7A	1.170 (14)
O2—C7	1.337 (14)	O2A—C7A	1.354 (15)
O2—C8	1.450 (16)	O2A—C8A	1.454 (16)
N1—C2	1.329 (15)	N1A—C2A	1.319 (15)
N1—C3	1.495 (14)	N1A—C3A	1.493 (14)
N1—C6	1.465 (14)	N1A—C6A	1.477 (15)
C1—H1A	0.9800	C1A—H1AA	0.9800
C1—H1B	0.9800	C1A—H1AB	0.9800
C1—H1C	0.9800	C1A—H1AC	0.9800
C1—C2	1.504 (19)	C1A—C2A	1.490 (18)
C3—H3A	0.9900	C3A—H3AA	0.9900
C3—H3B	0.9900	C3A—H3AB	0.9900
C3—C4	1.516 (18)	C3A—C4A	1.522 (18)
C4—H4A	0.9900	C4A—H4AA	0.9900
C4—H4B	0.9900	C4A—H4AB	0.9900
C4—C5	1.514 (19)	C4A—C5A	1.51 (2)
C5—H5A	0.9900	C5A—H5AA	0.9900
C5—H5B	0.9900	C5A—H5AB	0.9900
C5—C6	1.555 (16)	C5A—C6A	1.541 (17)
C6—H6	1.0000	C6A—H6A	1.0000
C6—C7	1.529 (15)	C6A—C7A	1.541 (15)
C8—H8A	0.9800	C8A—H8AA	0.9800
C8—H8B	0.9800	C8A—H8AB	0.9800
C8—H8C	0.9800	C8A—H8AC	0.9800
C7—O2—C8	114.7 (10)	C7A—O2A—C8A	113.3 (10)
C2—N1—C3	124.9 (10)	C2A—N1A—C3A	125.3 (9)
C2—N1—C6	123.3 (9)	C2A—N1A—C6A	123.3 (10)
C6—N1—C3	111.8 (9)	C6A—N1A—C3A	111.1 (9)
H1A—C1—H1B	109.5	H1AA—C1A—H1AB	109.5
H1A—C1—H1C	109.5	H1AA—C1A—H1AC	109.5
H1B—C1—H1C	109.5	H1AB—C1A—H1AC	109.5
C2—C1—H1A	109.5	C2A—C1A—H1AA	109.5
C2—C1—H1B	109.5	C2A—C1A—H1AB	109.5
C2—C1—H1C	109.5	C2A—C1A—H1AC	109.5
N1—C2—Se1	122.0 (9)	N1A—C2A—Se1A	122.3 (9)
N1—C2—C1	115.8 (10)	N1A—C2A—C1A	117.2 (11)
C1—C2—Se1	122.2 (8)	C1A—C2A—Se1A	120.4 (9)
N1—C3—H3A	111.1	N1A—C3A—H3AA	111.1
N1—C3—H3B	111.1	N1A—C3A—H3AB	111.1
N1—C3—C4	103.2 (10)	N1A—C3A—C4A	103.2 (9)
H3A—C3—H3B	109.1	H3AA—C3A—H3AB	109.1
C4—C3—H3A	111.1	C4A—C3A—H3AA	111.1
C4—C3—H3B	111.1	C4A—C3A—H3AB	111.1
C3—C4—H4A	111.0	C3A—C4A—H4AA	111.0
C3—C4—H4B	111.0	C3A—C4A—H4AB	111.0
H4A—C4—H4B	109.0	H4AA—C4A—H4AB	109.0
C5—C4—C3	104.0 (10)	C5A—C4A—C3A	103.9 (11)
C5—C4—H4A	111.0	C5A—C4A—H4AA	111.0
C5—C4—H4B	111.0	C5A—C4A—H4AB	111.0
C4—C5—H5A	111.1	C4A—C5A—H5AA	111.0
C4—C5—H5B	111.1	C4A—C5A—H5AB	111.0
C4—C5—C6	103.3 (10)	C4A—C5A—C6A	103.8 (9)
H5A—C5—H5B	109.1	H5AA—C5A—H5AB	109.0
C6—C5—H5A	111.1	C6A—C5A—H5AA	111.0
C6—C5—H5B	111.1	C6A—C5A—H5AB	111.0
N1—C6—C5	102.9 (9)	N1A—C6A—C5A	103.7 (9)
N1—C6—H6	111.1	N1A—C6A—H6A	110.9
N1—C6—C7	110.4 (8)	N1A—C6A—C7A	110.0 (9)
C5—C6—H6	111.1	C5A—C6A—H6A	110.9
C7—C6—C5	110.0 (9)	C5A—C6A—C7A	110.1 (9)
C7—C6—H6	111.1	C7A—C6A—H6A	110.9
O1—C7—O2	125.6 (10)	O1A—C7A—O2A	125.9 (11)
O1—C7—C6	125.5 (10)	O1A—C7A—C6A	126.3 (10)
O2—C7—C6	108.8 (9)	O2A—C7A—C6A	107.6 (9)
O2—C8—H8A	109.5	O2A—C8A—H8AA	109.5
O2—C8—H8B	109.5	O2A—C8A—H8AB	109.5
O2—C8—H8C	109.5	O2A—C8A—H8AC	109.5
H8A—C8—H8B	109.5	H8AA—C8A—H8AB	109.5
H8A—C8—H8C	109.5	H8AA—C8A—H8AC	109.5
H8B—C8—H8C	109.5	H8AB—C8A—H8AC	109.5
N1—C3—C4—C5	31.5 (11)	N1A—C3A—C4A—C5A	32.7 (12)
N1—C6—C7—O1	−25.3 (15)	N1A—C6A—C7A—O1A	−30.5 (16)
N1—C6—C7—O2	157.1 (9)	N1A—C6A—C7A—O2A	155.3 (9)
C2—N1—C3—C4	167.0 (10)	C2A—N1A—C3A—C4A	169.8 (10)
C2—N1—C6—C5	169.2 (10)	C2A—N1A—C6A—C5A	166.9 (9)
C2—N1—C6—C7	−73.5 (12)	C2A—N1A—C6A—C7A	−75.3 (12)
C3—N1—C2—Se1	−177.9 (8)	C3A—N1A—C2A—Se1A	179.8 (8)
C3—N1—C2—C1	5.1 (16)	C3A—N1A—C2A—C1A	1.6 (15)
C3—N1—C6—C5	−11.6 (11)	C3A—N1A—C6A—C5A	−8.4 (11)
C3—N1—C6—C7	105.7 (10)	C3A—N1A—C6A—C7A	109.4 (10)
C3—C4—C5—C6	−39.0 (11)	C3A—C4A—C5A—C6A	−38.3 (12)
C4—C5—C6—N1	30.9 (11)	C4A—C5A—C6A—N1A	28.6 (11)
C4—C5—C6—C7	−86.8 (11)	C4A—C5A—C6A—C7A	−89.0 (11)
C5—C6—C7—O1	87.6 (14)	C5A—C6A—C7A—O1A	83.2 (15)
C5—C6—C7—O2	−90.1 (11)	C5A—C6A—C7A—O2A	−91.0 (11)
C6—N1—C2—Se1	1.2 (14)	C6A—N1A—C2A—Se1A	5.2 (14)
C6—N1—C2—C1	−175.8 (11)	C6A—N1A—C2A—C1A	−173.0 (11)
C6—N1—C3—C4	−12.1 (12)	C6A—N1A—C3A—C4A	−15.0 (12)
C8—O2—C7—O1	0.0 (18)	C8A—O2A—C7A—O1A	3.5 (18)
C8—O2—C7—C6	177.7 (10)	C8A—O2A—C7A—C6A	177.7 (11)